FMO DATABASE

FMODB ID: 4JY1N

Calculation Name: 3EPU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3EPU

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZNP3

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	136
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1249992.463506
FMO2-HF: Nuclear repulsion	1193716.625396
FMO2-HF: Total energy	-56275.83811
FMO2-MP2: Total energy	-56437.246003

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-1.102	0.79	-0.019	-0.824	-1.049	0.002

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.008 / q_NPA : -0.016

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	SER	0	0.013	-0.029	3.816	0.422	2.164	-0.018	-0.809	-0.915	0.002
4	A	4	ARG	1	0.836	0.886	6.348	0.590	0.590	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.079	0.052	8.706	0.148	0.148	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.755	-0.836	7.274	-0.772	-0.772	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.873	0.928	4.703	-1.154	-1.004	-0.001	-0.015	-0.134	0.000
8	A	8	LEU	0	0.002	0.023	8.243	0.093	0.093	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.017	0.013	11.713	0.028	0.028	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.854	0.909	8.505	-0.726	-0.726	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.040	-0.025	11.110	0.000	0.000	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.042	0.014	13.205	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.027	-0.033	13.961	-0.034	-0.034	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.010	-0.017	11.833	0.007	0.007	0.000	0.000	0.000	0.000
15	A	15	LYS	1	0.752	0.888	15.847	-0.296	-0.296	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.006	0.000	18.512	-0.027	-0.027	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.090	-0.038	19.069	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	18	THR	0	0.028	0.016	18.132	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.817	-0.869	14.009	0.596	0.596	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.058	-0.037	14.809	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.015	0.002	16.379	-0.043	-0.043	0.000	0.000	0.000	0.000
22	A	22	VAL	0	0.029	0.000	11.339	0.035	0.035	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.039	-0.016	12.241	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.753	-0.875	13.780	-0.137	-0.137	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.959	-0.979	15.561	-0.191	-0.191	0.000	0.000	0.000	0.000
26	A	26	ASN	0	-0.077	-0.030	16.604	-0.044	-0.044	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.723	0.826	11.090	0.456	0.456	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.010	0.001	16.817	0.019	0.019	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.046	-0.017	16.861	0.021	0.021	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.012	0.007	18.962	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.019	-0.005	19.514	0.018	0.018	0.000	0.000	0.000	0.000
32	A	32	ILE	0	-0.014	-0.011	23.518	-0.011	-0.011	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.001	0.015	23.599	0.013	0.013	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.851	-0.936	27.426	0.085	0.085	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.107	-0.058	29.831	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.833	0.904	31.271	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.004	-0.016	29.302	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.908	0.956	27.984	-0.020	-0.020	0.000	0.000	0.000	0.000
39	A	39	ILE	0	0.031	0.026	23.051	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	40	LEU	0	-0.016	-0.007	22.330	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	LEU	0	0.004	0.010	17.955	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.003	-0.014	18.924	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	43	SER	0	0.023	0.022	14.005	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	44	THR	0	0.039	0.015	15.344	-0.056	-0.056	0.000	0.000	0.000	0.000
45	A	45	ASN	0	0.006	0.010	16.535	-0.070	-0.070	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.018	0.005	11.617	-0.054	-0.054	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.853	-0.930	12.758	-0.279	-0.279	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.003	0.000	15.501	0.036	0.036	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.026	-0.002	14.632	-0.036	-0.036	0.000	0.000	0.000	0.000
50	A	50	MET	0	-0.055	0.009	18.146	0.016	0.016	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.017	0.002	21.536	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	TYR	0	-0.002	-0.015	23.615	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.079	0.031	26.391	0.009	0.009	0.000	0.000	0.000	0.000
54	A	54	PHE	0	-0.037	-0.040	27.157	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	55	CYS	0	-0.049	-0.015	31.098	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.064	0.045	34.626	0.003	0.003	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.875	0.931	36.335	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.042	-0.016	39.111	0.003	0.003	0.000	0.000	0.000	0.000
59	A	59	PRO	0	0.000	0.000	42.167	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.905	-0.955	45.689	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.064	-0.031	47.683	0.002	0.002	0.000	0.000	0.000	0.000
62	A	62	ASN	0	0.101	0.082	49.268	0.000	0.000	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.083	-0.076	49.554	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.036	0.027	45.519	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.027	0.001	43.677	0.000	0.000	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.017	-0.009	43.604	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.871	-0.917	45.616	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.028	0.007	40.538	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.011	-0.010	40.069	0.000	0.000	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.018	-0.009	42.002	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	71	ALA	0	0.019	0.010	41.096	0.001	0.001	0.000	0.000	0.000	0.000
72	A	72	ASN	0	0.015	-0.001	36.137	0.004	0.004	0.000	0.000	0.000	0.000
73	A	73	LEU	0	-0.016	-0.001	38.653	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	74	TRP	0	0.006	0.017	37.764	0.001	0.001	0.000	0.000	0.000	0.000
75	A	75	PHE	0	0.048	0.018	35.182	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ALA	0	-0.014	0.013	35.702	0.001	0.001	0.000	0.000	0.000	0.000
77	A	77	GLU	-1	-0.996	-0.991	36.702	0.005	0.005	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.082	-0.045	37.176	0.005	0.005	0.000	0.000	0.000	0.000
79	A	79	ASN	0	-0.075	-0.028	32.152	0.000	0.000	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.006	0.004	31.787	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	PRO	0	-0.048	-0.037	29.674	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.006	0.005	30.719	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.013	0.002	32.452	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	CYS	0	-0.079	-0.043	32.511	-0.006	-0.006	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.006	-0.002	34.681	0.004	0.004	0.000	0.000	0.000	0.000
86	A	86	ASP	-1	-0.775	-0.854	32.075	-0.050	-0.050	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.019	-0.027	34.113	0.007	0.007	0.000	0.000	0.000	0.000
88	A	88	ASN	0	-0.066	-0.031	30.679	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.060	-0.032	31.951	0.005	0.005	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.016	-0.020	33.996	0.008	0.008	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.013	-0.016	33.623	0.005	0.005	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.012	-0.001	35.182	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.039	-0.022	29.584	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	LEU	0	0.014	0.022	31.409	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	ALA	0	-0.011	-0.008	27.956	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	LEU	0	0.031	0.012	25.132	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	97	ASN	0	-0.057	-0.036	21.678	0.000	0.000	0.000	0.000	0.000	0.000
98	A	98	PHE	0	0.039	0.023	16.734	0.013	0.013	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.049	0.022	18.811	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	100	LEU	0	-0.008	-0.029	12.411	0.028	0.028	0.000	0.000	0.000	0.000
101	A	101	ASN	0	-0.042	0.006	14.619	0.032	0.032	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.903	-0.951	16.056	0.007	0.007	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.033	-0.009	14.601	0.023	0.023	0.000	0.000	0.000	0.000
104	A	104	SER	0	-0.030	-0.042	15.230	0.030	0.030	0.000	0.000	0.000	0.000
105	A	105	VAL	0	0.031	0.002	15.380	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.787	-0.882	17.176	0.264	0.264	0.000	0.000	0.000	0.000
107	A	107	LYS	1	0.893	0.938	19.842	-0.115	-0.115	0.000	0.000	0.000	0.000
108	A	108	LEU	0	0.010	0.014	16.676	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.809	-0.912	20.297	0.199	0.199	0.000	0.000	0.000	0.000
110	A	110	CYS	0	-0.037	-0.005	22.489	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.874	-0.944	22.985	0.031	0.031	0.000	0.000	0.000	0.000
112	A	112	ILE	0	-0.028	-0.023	20.507	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.822	-0.894	24.852	0.079	0.079	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.009	-0.001	27.894	-0.007	-0.007	0.000	0.000	0.000	0.000
115	A	115	VAL	0	-0.012	-0.003	26.727	-0.007	-0.007	0.000	0.000	0.000	0.000
116	A	116	ILE	0	0.038	0.018	26.959	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.839	0.896	30.613	-0.070	-0.070	0.000	0.000	0.000	0.000
118	A	118	SER	0	-0.010	-0.005	32.565	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	119	MET	0	-0.033	-0.010	31.018	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.823	-0.876	34.435	0.041	0.041	0.000	0.000	0.000	0.000
121	A	121	ASN	0	0.018	-0.004	36.700	0.000	0.000	0.000	0.000	0.000	0.000
122	A	122	LEU	0	0.021	0.021	36.991	-0.003	-0.003	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.042	-0.030	35.394	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	124	HIS	0	-0.070	-0.047	40.222	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.003	0.016	41.347	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	126	LEU	0	-0.046	-0.032	41.080	-0.002	-0.002	0.000	0.000	0.000	0.000
127	A	127	GLN	0	-0.036	-0.001	43.439	0.000	0.000	0.000	0.000	0.000	0.000
128	A	128	ASP	-1	-0.923	-0.968	45.992	0.016	0.016	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.863	0.932	46.810	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.034	-0.004	49.066	-0.002	-0.002	0.000	0.000	0.000	0.000
131	A	131	ILE	0	-0.054	-0.027	46.432	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	132	THR	0	0.018	-0.006	43.312	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.026	0.010	38.394	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	134	ASP	-1	-0.840	-0.927	39.177	0.008	0.008	0.000	0.000	0.000	0.000
135	A	135	THR	0	0.003	-0.025	36.860	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	ASP	-1	-0.951	-0.938	34.474	0.013	0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)